Stage-dependent transcriptomic changes in human dermal fibroblast senescence model

Cellular senescence is a fundamental biological process that underlies organismal aging and age-related diseases; however, the temporal dynamics of gene expression during senescence remain unclear. This study investigated gene expression changes across aging progression and the molecular mechanisms involved using three replicative senescence models of human dermal fibroblasts, designated as young, middle, and old. RNA sequencing transcriptome analysis with two independent analytical pipelines revealed that the transcriptome profiles of the young and middle stages were similar, whereas that of the old stage was distinct. Differential expression analysis showed significant gene expression changes between the young and middle stages, with differentially expressed genes (DEGs) increasing as senescence progressed. STRING and Gene Ontology/Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated early activation of immune–inflammatory response clusters and decreases in structural maintenance genes. Using an alternative DEG set, non-negative matrix factorization (NMF) decomposed transcriptomes into distinct metagenes, with characteristic senescence-stage behaviors. NMF independently recapitulated immune–inflammatory activation and the loss of structural maintenance functions. These findings suggest that immune–inflammatory responses are engaged from early senescence, whereas cell adhesion and maintenance pathways decline progressively. These results identify early biomarkers and therapeutic targets, providing opportunities to delay or mitigate aging-related functional decline.